Protein Structure Refinement Guided by Atomic Packing Frustration Analysis

Molecular frustration: a hypothesis for regulation of viral infections

The recent revolution in imaging techniques and results from RNA footprinting in situ reveal how the bacteriophage MS2 genome regulates both particle assembly and genome release. We have proposed a model in which multiple packaging signal (PS) RNA-coat protein (CP) contacts orchestrate different stages of a viral life cycle. Programmed formation and release of specific PS contacts with CP regulates viral particle assembly and genome uncoating during cell entry. We hypothesize that molecular frustration, a concept introduced to understand protein folding, can be used to better rationalize how PSs function in both particle assembly and genome release. More broadly this concept may explain the directionality of viral life cycles, for example, the roles of host cofactors in HIV infection. We propose that this is a universal principle in virology that explains mechanisms of host-virus interaction and suggests diverse therapeutic interventions.

Computationally exploring the mechanism of bacteriophage T7 gp4 helicase translocating along ssDNA

Bacteriophage T7 gp4 helicase has served as a model system for understanding mechanisms of hexameric replicative helicase translocation. The mechanistic basis of how nucleoside 5'-triphosphate hydrolysis and translocation of gp4 helicase are coupled is not fully resolved. Here, we used a thermodynamically benchmarked coarse-grained protein force field, Associative memory, Water mediated, Structure and Energy Model (AWSEM), with the single-stranded DNA (ssDNA) force field 3SPN.2C to investigate gp4 translocation. We found that the adenosine 5'-triphosphate (ATP) at the subunit interface stabilizes the subunit-subunit interaction and inhibits subunit translocation. Hydrolysis of ATP to adenosine 5'-diphosphate enables the translocation of one subunit, and new ATP binding at the new subunit interface finalizes the subunit translocation. The LoopD2 and the N-terminal primase domain provide transient protein-protein and protein-DNA interactions that facilitate the large-scale subunit movement. The simulations of gp4 helicase both validate our coarse-grained protein-ssDNA force field and elucidate the molecular basis of replicative helicase translocation.

Exploring the Interplay between Disordered and Ordered Oligomer Channels on the Aggregation Energy Landscapes of α-Synuclein

The abnormal aggregation of α-synulcein is associated with multiple neurodegenerative diseases such as Parkinson's disease. The hydrophobic non-amyloid component (NAC) region of α-synuclein comprises the core of the fibril in vitro and in vivo. In this work, we study the aggregation landscape of the hydrophobic NAC region of α-synuclein using a transferrable coarse-grained force field, the associative memory water-mediated structure, and energy model (AWSEM). Using structural similarity, we can group metastable states on the free energy landscape of aggregation into three types of oligomers: disordered oligomers, prefibrillar oligomers with disordered tips, and ordered prefibrillar oligomers. The prefibrillar oligomers with disordered tips have more in-register parallel β strands than do the fully disordered oligomers but have fewer in-register parallel β strands than the ordered prefibrillar oligomers. Along with the ordered prefibrillar species, the disordered oligomeric states dominate at small oligomer sizes while the prefibrillar species with disordered tips thermodynamically dominate with the growth of oligomers. The topology of the aggregation landscape and observations in simulations suggest there is backtracking between ordered prefibrillar oligomers and other kinds of oligomers as the aggregation proceeds. The significant structural differences between the ordered prefibrillar oligomers and the disordered oligomers support the idea that the growth of these two kinds of oligomers involves kinetically independent parallel pathways. In contrast, the overall structural similarity between the fully ordered prefibrillar oligomers and the prefibrillar oligomers with disordered tips implies that two channels can interconvert on slower time scales. We also evaluate the effects of phosphorylation on the aggregation free energy landscape using statistical mechanical perturbation theory.

Frustration Dynamics and Electron-Transfer Reorganization Energies in Wild-Type and Mutant Azurins

Long-range electron tunneling through metalloproteins is facilitated by evolutionary tuning of donor–acceptor electronic couplings, formal electrochemical potentials, and active-site reorganization energies. Although the minimal frustration of the folding landscape enables this tuning, residual frustration in the vicinity of the metallocofactor can allow conformational fluctuations required for protein function. We show here that the constrained copper site in wild-type azurin is governed by an intricate pattern of minimally frustrated local and distant interactions that together enable rapid electron flow to and from the protein. In contrast, sluggish electron transfer reactions (unfavorable reorganization energies) of active-site azurin variants are attributable to increased frustration near to as well as distant from the copper site, along with an exaggerated oxidation-state dependence of both minimally and highly frustrated interaction patterns.